Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

Alex K. Shalek, Rahul Satija, Xian Adiconis, Rona S. Gertner, Jellert T. Gaublomme, Raktima Raychowdhury, Schraga Schwartz, Nir Yosef, Christine Malboeuf, Diana Lu, John J. Trombetta, Dave Gennert, Andreas Gnirke, Alon Goren, Nir Hacohen, Joshua Z. Levin, Hongkun Park, Aviv Regev

Research output: Contribution to journalArticle

Abstract

Recent molecular studies have shown that, even when derived from a seemingly homogenous population, individual cells can exhibit substantial differences in gene expression, protein levels and phenotypic output, with important functional consequences. Existing studies of cellular heterogeneity, however, have typically measured only a few pre-selected RNAs or proteins simultaneously, because genomic profiling methods could not be applied to single cells until very recently. Here we use single-cell RNA sequencing to investigate heterogeneity in the response of mouse bone-marrow-derived dendritic cells (BMDCs) to lipopolysaccharide. We find extensive, and previously unobserved, bimodal variation in messenger RNA abundance and splicing patterns, which we validate by RNA-fluorescence in situ hybridization for select transcripts. In particular, hundreds of key immune genes are bimodally expressed across cells, surprisingly even for genes that are very highly expressed at the population average. Moreover, splicing patterns demonstrate previously unobserved levels of heterogeneity between cells. Some of the observed bimodality can be attributed to closely related, yet distinct, known maturity states of BMDCs; other portions reflect differences in the usage of key regulatory circuits. For example, we identify a module of 137 highly variable, yet co-regulated, antiviral response genes. Using cells from knockout mice, we show that variability in this module may be propagated through an interferon feedback circuit, involving the transcriptional regulators Stat2 and Irf7. Our study demonstrates the power and promise of single-cell genomics in uncovering functional diversity between cells and in deciphering cell states and circuits.

Original languageEnglish (US)
Pages (from-to)236-240
Number of pages5
JournalNature
Volume498
Issue number7453
DOIs
StatePublished - 2013

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Dendritic Cells
Bone Marrow
RNA
Genes
RNA Splicing
RNA Sequence Analysis
Genomics
Fluorescence In Situ Hybridization
Knockout Mice
Interferons
Population
Antiviral Agents
Lipopolysaccharides
Proteins
Gene Expression

ASJC Scopus subject areas

  • General

Cite this

Shalek, A. K., Satija, R., Adiconis, X., Gertner, R. S., Gaublomme, J. T., Raychowdhury, R., ... Regev, A. (2013). Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature, 498(7453), 236-240. https://doi.org/10.1038/nature12172

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. / Shalek, Alex K.; Satija, Rahul; Adiconis, Xian; Gertner, Rona S.; Gaublomme, Jellert T.; Raychowdhury, Raktima; Schwartz, Schraga; Yosef, Nir; Malboeuf, Christine; Lu, Diana; Trombetta, John J.; Gennert, Dave; Gnirke, Andreas; Goren, Alon; Hacohen, Nir; Levin, Joshua Z.; Park, Hongkun; Regev, Aviv.

In: Nature, Vol. 498, No. 7453, 2013, p. 236-240.

Research output: Contribution to journalArticle

Shalek, AK, Satija, R, Adiconis, X, Gertner, RS, Gaublomme, JT, Raychowdhury, R, Schwartz, S, Yosef, N, Malboeuf, C, Lu, D, Trombetta, JJ, Gennert, D, Gnirke, A, Goren, A, Hacohen, N, Levin, JZ, Park, H & Regev, A 2013, 'Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells', Nature, vol. 498, no. 7453, pp. 236-240. https://doi.org/10.1038/nature12172
Shalek AK, Satija R, Adiconis X, Gertner RS, Gaublomme JT, Raychowdhury R et al. Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature. 2013;498(7453):236-240. https://doi.org/10.1038/nature12172
Shalek, Alex K. ; Satija, Rahul ; Adiconis, Xian ; Gertner, Rona S. ; Gaublomme, Jellert T. ; Raychowdhury, Raktima ; Schwartz, Schraga ; Yosef, Nir ; Malboeuf, Christine ; Lu, Diana ; Trombetta, John J. ; Gennert, Dave ; Gnirke, Andreas ; Goren, Alon ; Hacohen, Nir ; Levin, Joshua Z. ; Park, Hongkun ; Regev, Aviv. / Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. In: Nature. 2013 ; Vol. 498, No. 7453. pp. 236-240.
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